Starting phenix.real_space_refine on Wed Feb 4 07:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.map" model { file = "/net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh1_64151/02_2026/9uh1_64151.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5719 2.51 5 N 1592 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9084 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5190 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain: "B" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "F" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1973 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 9084 At special positions: 0 Unit cell: (99.45, 100.3, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1721 8.00 N 1592 7.00 C 5719 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 300.4 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 38.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.656A pdb=" N CYS A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.870A pdb=" N ALA A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.986A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.715A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.038A pdb=" N ASP A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 309 through 326 Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.641A pdb=" N GLU A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.967A pdb=" N ILE A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.731A pdb=" N ILE A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.809A pdb=" N VAL A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.596A pdb=" N ALA A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.798A pdb=" N ILE B 320 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.574A pdb=" N HIS B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.782A pdb=" N GLU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 522 removed outlier: 3.815A pdb=" N ARG B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 49 removed outlier: 3.869A pdb=" N ARG F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 removed outlier: 3.508A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.887A pdb=" N GLY F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET F 95 " --> pdb=" O ASP F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 91 through 95' Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.564A pdb=" N ASN F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS F 101 " --> pdb=" O ASP F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 169 through 187 removed outlier: 3.639A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 206 through 211 removed outlier: 3.645A pdb=" N THR F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 removed outlier: 3.575A pdb=" N VAL F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 278 removed outlier: 3.520A pdb=" N ALA F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP F 273 " --> pdb=" O CYS F 269 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 278 " --> pdb=" O PHE F 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.213A pdb=" N GLU A 108 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 91 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 110 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 139 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 351 removed outlier: 6.332A pdb=" N PHE A 347 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 338 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU A 349 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 399 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416 removed outlier: 4.088A pdb=" N GLY A 415 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 565 Processing sheet with id=AA7, first strand: chain 'A' and resid 669 through 673 removed outlier: 6.831A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS A 688 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 699 " --> pdb=" O CYS A 688 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.631A pdb=" N GLY A 705 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 331 removed outlier: 6.341A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 331 removed outlier: 6.341A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 454 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.839A pdb=" N ARG F 111 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL F 217 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 199 through 201 removed outlier: 5.458A pdb=" N TYR F 222 " --> pdb=" O CYS F 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 407 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1556 1.32 - 1.44: 2298 1.44 - 1.57: 5308 1.57 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 9249 Sorted by residual: bond pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " ideal model delta sigma weight residual 1.824 1.439 0.385 2.00e-02 2.50e+03 3.71e+02 bond pdb=" C3 BTN A 801 " pdb=" N2 BTN A 801 " ideal model delta sigma weight residual 1.362 1.555 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C3 BTN A 801 " pdb=" N1 BTN A 801 " ideal model delta sigma weight residual 1.358 1.507 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C2 BTN A 801 " pdb=" C4 BTN A 801 " ideal model delta sigma weight residual 1.534 1.682 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" C4 BTN A 801 " pdb=" N2 BTN A 801 " ideal model delta sigma weight residual 1.440 1.324 0.116 2.00e-02 2.50e+03 3.37e+01 ... (remaining 9244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 12452 3.30 - 6.60: 51 6.60 - 9.91: 5 9.91 - 13.21: 1 13.21 - 16.51: 1 Bond angle restraints: 12510 Sorted by residual: angle pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " pdb=" C6 BTN A 801 " ideal model delta sigma weight residual 88.98 105.49 -16.51 3.00e+00 1.11e-01 3.03e+01 angle pdb=" CA MET A 217 " pdb=" CB MET A 217 " pdb=" CG MET A 217 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" C MET F 145 " pdb=" N ASP F 146 " pdb=" CA ASP F 146 " ideal model delta sigma weight residual 120.31 115.55 4.76 1.52e+00 4.33e-01 9.82e+00 angle pdb=" CA LEU A 630 " pdb=" CB LEU A 630 " pdb=" CG LEU A 630 " ideal model delta sigma weight residual 116.30 126.61 -10.31 3.50e+00 8.16e-02 8.68e+00 angle pdb=" N GLU A 318 " pdb=" CA GLU A 318 " pdb=" CB GLU A 318 " ideal model delta sigma weight residual 110.12 114.41 -4.29 1.47e+00 4.63e-01 8.52e+00 ... (remaining 12505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5074 17.98 - 35.95: 465 35.95 - 53.93: 54 53.93 - 71.91: 17 71.91 - 89.89: 9 Dihedral angle restraints: 5619 sinusoidal: 2236 harmonic: 3383 Sorted by residual: dihedral pdb=" CA VAL A 216 " pdb=" C VAL A 216 " pdb=" N MET A 217 " pdb=" CA MET A 217 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP A 368 " pdb=" C ASP A 368 " pdb=" N LEU A 369 " pdb=" CA LEU A 369 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG B 432 " pdb=" C ARG B 432 " pdb=" N LYS B 433 " pdb=" CA LYS B 433 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1015 0.043 - 0.086: 283 0.086 - 0.129: 108 0.129 - 0.172: 11 0.172 - 0.214: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA MET F 145 " pdb=" N MET F 145 " pdb=" C MET F 145 " pdb=" CB MET F 145 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1416 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 446 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 447 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 296 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" CG ASP B 296 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP B 296 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP B 296 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 296 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ASP B 296 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 296 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG B 297 " 0.008 2.00e-02 2.50e+03 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1573 2.77 - 3.30: 8695 3.30 - 3.83: 14493 3.83 - 4.37: 16113 4.37 - 4.90: 28784 Nonbonded interactions: 69658 Sorted by model distance: nonbonded pdb=" OE1 GLU A 487 " pdb=" OH TYR A 508 " model vdw 2.237 3.040 nonbonded pdb=" NH2 ARG F 117 " pdb=" O LEU F 278 " model vdw 2.286 3.120 nonbonded pdb=" O ASP A 235 " pdb=" OG1 THR A 238 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR B 451 " pdb=" OD2 ASP B 518 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 420 " pdb=" OH TYR A 473 " model vdw 2.290 3.040 ... (remaining 69653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.006 0.385 9250 Z= 0.334 Angle : 0.625 16.510 12510 Z= 0.316 Chirality : 0.045 0.214 1419 Planarity : 0.004 0.039 1634 Dihedral : 14.049 89.886 3443 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1175 helix: 0.19 (0.26), residues: 403 sheet: 0.47 (0.37), residues: 188 loop : -1.20 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.009 0.001 TYR A 455 PHE 0.019 0.001 PHE A 263 TRP 0.019 0.002 TRP A 233 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 9249) covalent geometry : angle 0.62500 (12510) hydrogen bonds : bond 0.15988 ( 388) hydrogen bonds : angle 5.91893 ( 1143) Misc. bond : bond 0.13075 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0781 time to fit residues: 13.6407 Evaluate side-chains 100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 472 ASN ** 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 = 0.4164 r_free = 0.4164 target = 0.194583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156188 restraints weight = 12152.222| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.16 r_work: 0.3369 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9250 Z= 0.120 Angle : 0.577 7.735 12510 Z= 0.298 Chirality : 0.045 0.150 1419 Planarity : 0.003 0.038 1634 Dihedral : 4.775 42.301 1294 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.02 % Allowed : 9.09 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1175 helix: 0.49 (0.26), residues: 415 sheet: 0.05 (0.33), residues: 226 loop : -1.09 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.009 0.001 TYR A 420 PHE 0.012 0.001 PHE B 384 TRP 0.010 0.001 TRP A 559 HIS 0.003 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9249) covalent geometry : angle 0.57676 (12510) hydrogen bonds : bond 0.03878 ( 388) hydrogen bonds : angle 4.54861 ( 1143) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: A 472 ASN cc_start: 0.8504 (m-40) cc_final: 0.8268 (m-40) REVERT: A 697 ASN cc_start: 0.8758 (t0) cc_final: 0.8387 (t0) REVERT: F 84 MET cc_start: 0.5095 (ptp) cc_final: 0.4567 (ptp) REVERT: F 95 MET cc_start: 0.3976 (ppp) cc_final: 0.3534 (ppp) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.0678 time to fit residues: 12.4177 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 48 optimal weight: 0.2980 chunk 36 optimal weight: 0.0040 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** A 472 ASN ** 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 = 0.4161 r_free = 0.4161 target = 0.194655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.154772 restraints weight = 12172.631| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.36 r_work: 0.3412 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9250 Z= 0.103 Angle : 0.545 8.033 12510 Z= 0.282 Chirality : 0.044 0.149 1419 Planarity : 0.003 0.039 1634 Dihedral : 4.315 52.389 1294 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.63 % Allowed : 12.16 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1175 helix: 0.51 (0.26), residues: 428 sheet: 0.31 (0.35), residues: 205 loop : -1.02 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.009 0.001 TYR A 420 PHE 0.013 0.001 PHE A 263 TRP 0.006 0.001 TRP A 559 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9249) covalent geometry : angle 0.54534 (12510) hydrogen bonds : bond 0.03314 ( 388) hydrogen bonds : angle 4.27721 ( 1143) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.387 Fit side-chains REVERT: A 289 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6380 (tt0) REVERT: A 371 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: A 690 ILE cc_start: 0.8677 (mt) cc_final: 0.8430 (tp) REVERT: A 697 ASN cc_start: 0.8627 (t0) cc_final: 0.8229 (t0) REVERT: B 463 MET cc_start: 0.6242 (tmm) cc_final: 0.5935 (tmm) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 0.0798 time to fit residues: 15.3897 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 546 ASN F 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139345 restraints weight = 12293.883| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.11 r_work: 0.3262 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9250 Z= 0.208 Angle : 0.648 9.401 12510 Z= 0.335 Chirality : 0.048 0.162 1419 Planarity : 0.004 0.038 1634 Dihedral : 4.787 49.163 1294 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.96 % Allowed : 13.07 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1175 helix: 0.34 (0.26), residues: 419 sheet: 0.05 (0.33), residues: 228 loop : -1.09 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.012 0.001 TYR A 401 PHE 0.016 0.002 PHE F 224 TRP 0.028 0.002 TRP A 559 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9249) covalent geometry : angle 0.64790 (12510) hydrogen bonds : bond 0.04971 ( 388) hydrogen bonds : angle 4.54122 ( 1143) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.336 Fit side-chains REVERT: A 289 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: A 516 MET cc_start: 0.7817 (mmm) cc_final: 0.7547 (mmm) REVERT: A 690 ILE cc_start: 0.8668 (mt) cc_final: 0.8342 (tp) REVERT: A 697 ASN cc_start: 0.8591 (t0) cc_final: 0.8154 (t0) REVERT: F 114 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7304 (mt) outliers start: 29 outliers final: 19 residues processed: 119 average time/residue: 0.0787 time to fit residues: 14.1158 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN ** F 58 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151907 restraints weight = 12179.529| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.27 r_work: 0.3298 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9250 Z= 0.139 Angle : 0.592 9.680 12510 Z= 0.305 Chirality : 0.045 0.150 1419 Planarity : 0.003 0.037 1634 Dihedral : 4.612 46.587 1294 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.25 % Allowed : 14.61 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1175 helix: 0.43 (0.26), residues: 418 sheet: 0.07 (0.33), residues: 228 loop : -1.03 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 117 TYR 0.008 0.001 TYR A 420 PHE 0.014 0.001 PHE F 274 TRP 0.013 0.001 TRP A 559 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9249) covalent geometry : angle 0.59172 (12510) hydrogen bonds : bond 0.03937 ( 388) hydrogen bonds : angle 4.35105 ( 1143) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.437 Fit side-chains REVERT: A 289 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: A 690 ILE cc_start: 0.8760 (mt) cc_final: 0.8468 (tp) REVERT: A 697 ASN cc_start: 0.8503 (t0) cc_final: 0.8077 (t0) REVERT: F 95 MET cc_start: 0.3565 (ppp) cc_final: 0.3191 (ppp) REVERT: F 114 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7175 (mt) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.0854 time to fit residues: 15.1960 Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 0.0000 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN ** F 58 GLN ** 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 = 0.4131 r_free = 0.4131 target = 0.191817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151209 restraints weight = 12062.229| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.32 r_work: 0.3312 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9250 Z= 0.110 Angle : 0.567 10.379 12510 Z= 0.290 Chirality : 0.044 0.172 1419 Planarity : 0.003 0.037 1634 Dihedral : 4.392 44.578 1294 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.35 % Allowed : 16.14 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1175 helix: 0.53 (0.26), residues: 419 sheet: 0.08 (0.33), residues: 228 loop : -0.98 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.009 0.001 TYR A 420 PHE 0.011 0.001 PHE B 384 TRP 0.005 0.001 TRP B 531 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9249) covalent geometry : angle 0.56715 (12510) hydrogen bonds : bond 0.03315 ( 388) hydrogen bonds : angle 4.18470 ( 1143) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.441 Fit side-chains REVERT: A 217 MET cc_start: 0.5191 (mmt) cc_final: 0.4864 (mmt) REVERT: A 229 MET cc_start: 0.7395 (ptp) cc_final: 0.6944 (ptp) REVERT: A 289 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: A 690 ILE cc_start: 0.8705 (mt) cc_final: 0.8422 (tp) REVERT: A 697 ASN cc_start: 0.8495 (t0) cc_final: 0.8088 (t0) REVERT: F 95 MET cc_start: 0.3545 (ppp) cc_final: 0.2740 (ppp) REVERT: F 114 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7070 (mt) REVERT: F 124 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7546 (mm-40) REVERT: F 262 GLU cc_start: 0.7314 (mp0) cc_final: 0.6920 (mp0) outliers start: 23 outliers final: 13 residues processed: 122 average time/residue: 0.0805 time to fit residues: 14.5867 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 124 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 696 GLN F 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151979 restraints weight = 12090.312| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.26 r_work: 0.3356 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9250 Z= 0.124 Angle : 0.577 8.649 12510 Z= 0.293 Chirality : 0.044 0.165 1419 Planarity : 0.003 0.037 1634 Dihedral : 4.377 44.443 1294 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.04 % Allowed : 17.98 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1175 helix: 0.59 (0.26), residues: 419 sheet: 0.05 (0.33), residues: 226 loop : -0.95 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 69 TYR 0.008 0.001 TYR A 420 PHE 0.015 0.001 PHE A 263 TRP 0.005 0.001 TRP B 531 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9249) covalent geometry : angle 0.57705 (12510) hydrogen bonds : bond 0.03465 ( 388) hydrogen bonds : angle 4.14519 ( 1143) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.414 Fit side-chains REVERT: A 85 MET cc_start: 0.7955 (mtp) cc_final: 0.7738 (mtp) REVERT: A 217 MET cc_start: 0.5386 (mmt) cc_final: 0.5089 (mmt) REVERT: A 229 MET cc_start: 0.7349 (ptp) cc_final: 0.6946 (ptp) REVERT: A 289 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: A 690 ILE cc_start: 0.8725 (mt) cc_final: 0.8450 (tp) REVERT: A 697 ASN cc_start: 0.8461 (t0) cc_final: 0.8109 (t0) REVERT: F 95 MET cc_start: 0.3379 (ppp) cc_final: 0.2716 (ppp) REVERT: F 114 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7093 (mt) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.0838 time to fit residues: 14.7298 Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 33 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 696 GLN ** 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 = 0.4103 r_free = 0.4103 target = 0.189146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148680 restraints weight = 12099.336| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.46 r_work: 0.3291 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9250 Z= 0.155 Angle : 0.620 12.315 12510 Z= 0.314 Chirality : 0.046 0.187 1419 Planarity : 0.003 0.037 1634 Dihedral : 4.557 43.369 1294 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.45 % Allowed : 17.98 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1175 helix: 0.51 (0.26), residues: 420 sheet: 0.09 (0.33), residues: 223 loop : -1.02 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 69 TYR 0.009 0.001 TYR A 473 PHE 0.015 0.001 PHE A 263 TRP 0.006 0.001 TRP B 531 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9249) covalent geometry : angle 0.62022 (12510) hydrogen bonds : bond 0.04007 ( 388) hydrogen bonds : angle 4.26418 ( 1143) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.315 Fit side-chains REVERT: A 217 MET cc_start: 0.5649 (mmt) cc_final: 0.5389 (mmt) REVERT: A 229 MET cc_start: 0.7322 (ptp) cc_final: 0.6921 (ptp) REVERT: A 289 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: A 516 MET cc_start: 0.8026 (mmm) cc_final: 0.7731 (mmm) REVERT: A 690 ILE cc_start: 0.8748 (mt) cc_final: 0.8501 (tp) REVERT: A 697 ASN cc_start: 0.8479 (t0) cc_final: 0.8083 (t0) REVERT: F 95 MET cc_start: 0.3713 (ppp) cc_final: 0.3060 (ppp) REVERT: F 114 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7177 (mt) REVERT: F 124 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7626 (mm-40) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.0758 time to fit residues: 13.6018 Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 65 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151298 restraints weight = 12063.656| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.43 r_work: 0.3336 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9250 Z= 0.143 Angle : 0.605 9.012 12510 Z= 0.309 Chirality : 0.045 0.164 1419 Planarity : 0.003 0.038 1634 Dihedral : 4.502 40.934 1294 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.45 % Allowed : 17.98 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1175 helix: 0.57 (0.26), residues: 419 sheet: 0.07 (0.33), residues: 223 loop : -1.03 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.008 0.001 TYR A 473 PHE 0.015 0.001 PHE A 263 TRP 0.005 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9249) covalent geometry : angle 0.60540 (12510) hydrogen bonds : bond 0.03760 ( 388) hydrogen bonds : angle 4.20811 ( 1143) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.369 Fit side-chains REVERT: A 217 MET cc_start: 0.5423 (mmt) cc_final: 0.4720 (mmt) REVERT: A 229 MET cc_start: 0.7134 (ptp) cc_final: 0.6524 (mtm) REVERT: A 289 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 516 MET cc_start: 0.7680 (mmm) cc_final: 0.7421 (mmm) REVERT: A 690 ILE cc_start: 0.8795 (mt) cc_final: 0.8562 (tp) REVERT: A 697 ASN cc_start: 0.8543 (t0) cc_final: 0.8127 (t0) REVERT: B 309 GLU cc_start: 0.7234 (mp0) cc_final: 0.6854 (mp0) REVERT: F 95 MET cc_start: 0.3561 (ppp) cc_final: 0.2989 (ppp) REVERT: F 105 ASP cc_start: 0.6894 (t0) cc_final: 0.6615 (t0) REVERT: F 114 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7139 (mt) REVERT: F 124 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7538 (mm-40) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.0825 time to fit residues: 14.6118 Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150033 restraints weight = 12067.881| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.56 r_work: 0.3291 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9250 Z= 0.140 Angle : 0.607 9.199 12510 Z= 0.309 Chirality : 0.045 0.187 1419 Planarity : 0.003 0.038 1634 Dihedral : 4.482 38.613 1294 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.35 % Allowed : 18.28 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1175 helix: 0.56 (0.26), residues: 420 sheet: 0.04 (0.33), residues: 223 loop : -1.02 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.008 0.001 TYR A 473 PHE 0.015 0.001 PHE A 263 TRP 0.005 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9249) covalent geometry : angle 0.60669 (12510) hydrogen bonds : bond 0.03750 ( 388) hydrogen bonds : angle 4.19708 ( 1143) Misc. bond : bond 0.00016 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.285 Fit side-chains REVERT: A 217 MET cc_start: 0.5796 (mmt) cc_final: 0.4934 (mmt) REVERT: A 229 MET cc_start: 0.7289 (ptp) cc_final: 0.6552 (mtm) REVERT: A 289 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: A 516 MET cc_start: 0.8024 (mmm) cc_final: 0.7758 (mmm) REVERT: A 690 ILE cc_start: 0.8782 (mt) cc_final: 0.8512 (tp) REVERT: A 697 ASN cc_start: 0.8497 (t0) cc_final: 0.8146 (t0) REVERT: B 309 GLU cc_start: 0.7190 (mp0) cc_final: 0.6684 (mp0) REVERT: B 463 MET cc_start: 0.6589 (tmm) cc_final: 0.6008 (tmm) REVERT: F 95 MET cc_start: 0.3733 (ppp) cc_final: 0.3110 (ppp) REVERT: F 105 ASP cc_start: 0.6997 (t0) cc_final: 0.6647 (t0) REVERT: F 114 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7087 (mt) REVERT: F 124 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7636 (mm-40) outliers start: 23 outliers final: 19 residues processed: 115 average time/residue: 0.0837 time to fit residues: 14.3411 Evaluate side-chains 122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.0570 chunk 114 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.192137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151869 restraints weight = 11942.361| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.30 r_work: 0.3362 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9250 Z= 0.124 Angle : 0.595 9.381 12510 Z= 0.303 Chirality : 0.045 0.179 1419 Planarity : 0.003 0.038 1634 Dihedral : 4.377 37.006 1294 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.15 % Allowed : 18.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.24), residues: 1175 helix: 0.62 (0.26), residues: 420 sheet: 0.04 (0.34), residues: 223 loop : -0.99 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.008 0.001 TYR A 444 PHE 0.015 0.001 PHE A 263 TRP 0.005 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9249) covalent geometry : angle 0.59458 (12510) hydrogen bonds : bond 0.03489 ( 388) hydrogen bonds : angle 4.14313 ( 1143) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.52 seconds wall clock time: 44 minutes 35.42 seconds (2675.42 seconds total)