Starting phenix.real_space_refine on Wed Feb 4 05:13:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9d_70246/02_2026/9o9d_70246.map" } resolution = 2.44 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= 0.016 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 P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 5517 2.51 5 N 1493 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s 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: 8686 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4322 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 22, 'TRANS': 548} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'PHE:plan': 2, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4120 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 20, 'TRANS': 523} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.43, per 1000 atoms: 0.28 Number of scatterers: 8686 At special positions: 0 Unit cell: (72.3187, 88.1693, 139.684, 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) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1630 8.00 N 1493 7.00 C 5517 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: 0.96 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 71.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.585A pdb=" N CYS A 179 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 217 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 220 through 269 removed outlier: 3.558A pdb=" N MET A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 273 No H-bonds generated for 'chain 'A' and resid 272 through 273' Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 290 through 324 removed outlier: 4.349A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.761A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 372 removed outlier: 3.539A pdb=" N LYS A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 436 removed outlier: 4.054A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 475 removed outlier: 3.610A pdb=" N THR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 674 through 687 removed outlier: 3.860A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.780A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.970A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.925A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 removed outlier: 3.543A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 338 removed outlier: 3.663A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 401 removed outlier: 3.525A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 439 removed outlier: 4.009A pdb=" N ILE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.773A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.581A pdb=" N TYR B 537 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.013A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 623 removed outlier: 4.541A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.512A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.847A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.847A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 581 through 583 removed outlier: 6.759A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 493 removed outlier: 6.621A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.476A pdb=" N THR B 499 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL B 674 " --> pdb=" O GLN B 681 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 558 through 559 607 hydrogen bonds defined for protein. 1764 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: 1.49 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2878 1.35 - 1.46: 1930 1.46 - 1.58: 3966 1.58 - 1.70: 9 1.70 - 1.82: 62 Bond restraints: 8845 Sorted by residual: bond pdb=" CA LEU B 294 " pdb=" C LEU B 294 " ideal model delta sigma weight residual 1.524 1.609 -0.085 1.32e-02 5.74e+03 4.16e+01 bond pdb=" C TYR B 415 " pdb=" N GLN B 416 " ideal model delta sigma weight residual 1.334 1.400 -0.065 1.27e-02 6.20e+03 2.63e+01 bond pdb=" C GLN B 416 " pdb=" N GLU B 417 " ideal model delta sigma weight residual 1.335 1.289 0.046 1.31e-02 5.83e+03 1.24e+01 bond pdb=" N LEU B 459 " pdb=" CA LEU B 459 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.71e+00 bond pdb=" N THR B 458 " pdb=" CA THR B 458 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.32e-02 5.74e+03 7.26e+00 ... (remaining 8840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11926 2.64 - 5.29: 88 5.29 - 7.93: 19 7.93 - 10.58: 4 10.58 - 13.22: 1 Bond angle restraints: 12038 Sorted by residual: angle pdb=" N LEU B 295 " pdb=" CA LEU B 295 " pdb=" C LEU B 295 " ideal model delta sigma weight residual 111.11 124.33 -13.22 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N LEU B 392 " pdb=" CA LEU B 392 " pdb=" C LEU B 392 " ideal model delta sigma weight residual 111.14 102.95 8.19 1.08e+00 8.57e-01 5.74e+01 angle pdb=" N THR B 293 " pdb=" CA THR B 293 " pdb=" C THR B 293 " ideal model delta sigma weight residual 111.14 103.24 7.90 1.08e+00 8.57e-01 5.35e+01 angle pdb=" N GLN A 432 " pdb=" CA GLN A 432 " pdb=" C GLN A 432 " ideal model delta sigma weight residual 111.07 117.40 -6.33 1.07e+00 8.73e-01 3.50e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 111.07 117.39 -6.32 1.07e+00 8.73e-01 3.49e+01 ... (remaining 12033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4771 17.91 - 35.82: 404 35.82 - 53.73: 117 53.73 - 71.64: 19 71.64 - 89.55: 14 Dihedral angle restraints: 5325 sinusoidal: 2047 harmonic: 3278 Sorted by residual: dihedral pdb=" C LEU B 294 " pdb=" N LEU B 294 " pdb=" CA LEU B 294 " pdb=" CB LEU B 294 " ideal model delta harmonic sigma weight residual -122.60 -133.58 10.98 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" CA ASN B 563 " pdb=" C ASN B 563 " pdb=" N ILE B 564 " pdb=" CA ILE B 564 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA HIS A 578 " pdb=" C HIS A 578 " pdb=" N ARG A 579 " pdb=" CA ARG A 579 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1280 0.064 - 0.128: 125 0.128 - 0.191: 3 0.191 - 0.255: 2 0.255 - 0.319: 4 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA LEU B 295 " pdb=" N LEU B 295 " pdb=" C LEU B 295 " pdb=" CB LEU B 295 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA LEU B 294 " pdb=" N LEU B 294 " pdb=" C LEU B 294 " pdb=" CB LEU B 294 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA THR B 293 " pdb=" N THR B 293 " pdb=" C THR B 293 " pdb=" CB THR B 293 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1411 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 428 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C TYR A 428 " 0.071 2.00e-02 2.50e+03 pdb=" O TYR A 428 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 429 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 294 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C LEU B 294 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 294 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 295 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 59 " 0.011 2.00e-02 2.50e+03 1.27e-02 2.81e+00 pdb=" CG PHE D 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE D 59 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 59 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE D 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 59 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 59 " -0.000 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 23 2.58 - 3.16: 7040 3.16 - 3.74: 13388 3.74 - 4.32: 17765 4.32 - 4.90: 30310 Nonbonded interactions: 68526 Sorted by model distance: nonbonded pdb=" OE1 GLN B 551 " pdb="MG MG B 702 " model vdw 2.002 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A1002 " model vdw 2.016 2.170 nonbonded pdb=" OE1 GLN A 586 " pdb="MG MG A1002 " model vdw 2.071 2.170 nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 2.075 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.076 2.170 ... (remaining 68521 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: 3.450 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 0.085 8845 Z= 0.179 Angle : 0.620 13.220 12038 Z= 0.387 Chirality : 0.041 0.319 1414 Planarity : 0.003 0.041 1541 Dihedral : 15.497 89.548 3221 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.55 % Allowed : 10.30 % Favored : 89.15 % Cbeta Deviations : 0.10 % 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: 3.14 (0.25), residues: 1134 helix: 2.75 (0.19), residues: 743 sheet: 2.40 (0.60), residues: 76 loop : 0.32 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.011 0.001 TYR B 172 PHE 0.029 0.001 PHE D 59 TRP 0.008 0.001 TRP A 348 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8845) covalent geometry : angle 0.62048 (12038) hydrogen bonds : bond 0.16799 ( 605) hydrogen bonds : angle 4.59807 ( 1764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6544 (tpt170) cc_final: 0.5447 (pmm-80) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.5585 time to fit residues: 53.5705 Evaluate side-chains 84 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 433 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3444 r_free = 0.3444 target = 0.104895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077133 restraints weight = 13347.111| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.30 r_work: 0.2855 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8845 Z= 0.138 Angle : 0.492 6.076 12038 Z= 0.259 Chirality : 0.038 0.147 1414 Planarity : 0.003 0.033 1541 Dihedral : 7.945 84.135 1303 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.21 % Allowed : 9.52 % Favored : 88.26 % 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: 3.20 (0.25), residues: 1134 helix: 2.81 (0.19), residues: 760 sheet: 2.08 (0.60), residues: 76 loop : 0.27 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.013 0.001 TYR A 428 PHE 0.012 0.002 PHE B 156 TRP 0.007 0.001 TRP B 139 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8845) covalent geometry : angle 0.49239 (12038) hydrogen bonds : bond 0.06593 ( 605) hydrogen bonds : angle 3.79919 ( 1764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6421 (tpt170) cc_final: 0.5773 (pmt170) REVERT: A 301 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: B 139 TRP cc_start: 0.8289 (t-100) cc_final: 0.7942 (t60) REVERT: B 316 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7986 (tt0) outliers start: 20 outliers final: 5 residues processed: 95 average time/residue: 0.5422 time to fit residues: 55.6572 Evaluate side-chains 89 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3423 r_free = 0.3423 target = 0.103451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075602 restraints weight = 13255.650| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.30 r_work: 0.2827 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8845 Z= 0.149 Angle : 0.485 5.905 12038 Z= 0.256 Chirality : 0.038 0.147 1414 Planarity : 0.003 0.033 1541 Dihedral : 7.740 84.286 1296 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.21 % Allowed : 10.08 % Favored : 87.71 % 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: 3.17 (0.25), residues: 1134 helix: 2.81 (0.19), residues: 763 sheet: 1.98 (0.61), residues: 76 loop : 0.18 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.012 0.001 TYR A 309 PHE 0.030 0.002 PHE D 59 TRP 0.005 0.001 TRP B 139 HIS 0.006 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8845) covalent geometry : angle 0.48537 (12038) hydrogen bonds : bond 0.06782 ( 605) hydrogen bonds : angle 3.69130 ( 1764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6435 (tpt170) cc_final: 0.5737 (pmt170) REVERT: A 301 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: A 358 GLU cc_start: 0.8749 (tt0) cc_final: 0.8314 (mt-10) REVERT: B 139 TRP cc_start: 0.8260 (t-100) cc_final: 0.7921 (t60) REVERT: B 286 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7994 (mm) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.5608 time to fit residues: 57.9876 Evaluate side-chains 97 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 433 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3427 r_free = 0.3427 target = 0.103627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.075733 restraints weight = 13436.266| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.32 r_work: 0.2825 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.146 Angle : 0.483 6.572 12038 Z= 0.254 Chirality : 0.038 0.149 1414 Planarity : 0.003 0.032 1541 Dihedral : 7.662 84.591 1296 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.66 % Allowed : 10.63 % Favored : 86.71 % 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: 3.19 (0.25), residues: 1134 helix: 2.85 (0.19), residues: 763 sheet: 1.89 (0.60), residues: 76 loop : 0.16 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.012 0.001 TYR A 309 PHE 0.014 0.002 PHE B 588 TRP 0.004 0.001 TRP A 348 HIS 0.006 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8845) covalent geometry : angle 0.48340 (12038) hydrogen bonds : bond 0.06631 ( 605) hydrogen bonds : angle 3.64329 ( 1764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.360 Fit side-chains REVERT: A 175 ARG cc_start: 0.6454 (tpt170) cc_final: 0.5723 (pmt170) REVERT: A 301 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 358 GLU cc_start: 0.8750 (tt0) cc_final: 0.8300 (mt-10) REVERT: A 565 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (m-30) REVERT: B 139 TRP cc_start: 0.8247 (t-100) cc_final: 0.7935 (t60) REVERT: B 286 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 441 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (pt0) outliers start: 24 outliers final: 10 residues processed: 97 average time/residue: 0.5250 time to fit residues: 55.0580 Evaluate side-chains 94 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3421 r_free = 0.3421 target = 0.103315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075562 restraints weight = 13412.850| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.29 r_work: 0.2830 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.145 Angle : 0.494 7.499 12038 Z= 0.256 Chirality : 0.038 0.145 1414 Planarity : 0.003 0.033 1541 Dihedral : 7.633 84.784 1296 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.77 % Allowed : 11.85 % Favored : 85.38 % 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: 3.22 (0.25), residues: 1134 helix: 2.88 (0.19), residues: 763 sheet: 1.86 (0.61), residues: 76 loop : 0.14 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.013 0.001 TYR B 376 PHE 0.029 0.002 PHE D 59 TRP 0.004 0.001 TRP A 322 HIS 0.005 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8845) covalent geometry : angle 0.49398 (12038) hydrogen bonds : bond 0.06565 ( 605) hydrogen bonds : angle 3.61253 ( 1764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6503 (tpt170) cc_final: 0.5767 (pmt170) REVERT: A 301 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: A 358 GLU cc_start: 0.8763 (tt0) cc_final: 0.8322 (mt-10) REVERT: A 565 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8909 (m-30) REVERT: B 139 TRP cc_start: 0.8199 (t-100) cc_final: 0.7907 (t60) REVERT: B 286 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7959 (mm) REVERT: B 441 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8110 (pt0) outliers start: 25 outliers final: 11 residues processed: 98 average time/residue: 0.5457 time to fit residues: 57.7753 Evaluate side-chains 95 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3431 r_free = 0.3431 target = 0.103987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076284 restraints weight = 13436.547| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.30 r_work: 0.2844 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8845 Z= 0.134 Angle : 0.480 7.698 12038 Z= 0.249 Chirality : 0.038 0.144 1414 Planarity : 0.003 0.033 1541 Dihedral : 7.515 83.415 1296 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.55 % Allowed : 12.40 % Favored : 85.05 % 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: 3.28 (0.25), residues: 1134 helix: 2.94 (0.19), residues: 763 sheet: 1.86 (0.61), residues: 76 loop : 0.11 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 380 TYR 0.012 0.001 TYR B 376 PHE 0.013 0.001 PHE B 588 TRP 0.005 0.001 TRP A 322 HIS 0.005 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8845) covalent geometry : angle 0.48003 (12038) hydrogen bonds : bond 0.06280 ( 605) hydrogen bonds : angle 3.55475 ( 1764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6498 (tpt170) cc_final: 0.5793 (pmt170) REVERT: A 301 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: A 358 GLU cc_start: 0.8757 (tt0) cc_final: 0.8317 (mt-10) REVERT: A 565 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8859 (m-30) REVERT: A 589 GLN cc_start: 0.8934 (mt0) cc_final: 0.8650 (mt0) REVERT: B 139 TRP cc_start: 0.8158 (t-100) cc_final: 0.7869 (t60) REVERT: B 286 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7909 (mm) REVERT: B 441 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8112 (pt0) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 0.5428 time to fit residues: 55.5790 Evaluate side-chains 97 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3416 r_free = 0.3416 target = 0.102911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075156 restraints weight = 13463.241| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.30 r_work: 0.2816 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8845 Z= 0.157 Angle : 0.509 8.362 12038 Z= 0.262 Chirality : 0.039 0.145 1414 Planarity : 0.003 0.033 1541 Dihedral : 7.671 86.143 1296 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.66 % Allowed : 12.85 % Favored : 84.50 % 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: 3.19 (0.25), residues: 1134 helix: 2.89 (0.19), residues: 763 sheet: 1.83 (0.60), residues: 76 loop : 0.04 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 380 TYR 0.013 0.001 TYR B 376 PHE 0.030 0.002 PHE D 59 TRP 0.006 0.001 TRP A 322 HIS 0.005 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8845) covalent geometry : angle 0.50877 (12038) hydrogen bonds : bond 0.06712 ( 605) hydrogen bonds : angle 3.60885 ( 1764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6609 (tpt170) cc_final: 0.5822 (pmt170) REVERT: A 301 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: A 358 GLU cc_start: 0.8774 (tt0) cc_final: 0.8337 (mt-10) REVERT: A 565 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8911 (m-30) REVERT: A 589 GLN cc_start: 0.8933 (mt0) cc_final: 0.8640 (mt0) REVERT: B 139 TRP cc_start: 0.8186 (t-100) cc_final: 0.7892 (t60) REVERT: B 286 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 441 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8158 (pt0) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 0.4993 time to fit residues: 51.8266 Evaluate side-chains 97 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3435 r_free = 0.3435 target = 0.104307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076542 restraints weight = 13279.379| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.29 r_work: 0.2846 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8845 Z= 0.129 Angle : 0.485 8.544 12038 Z= 0.249 Chirality : 0.037 0.142 1414 Planarity : 0.003 0.032 1541 Dihedral : 7.448 82.650 1296 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.99 % Allowed : 13.84 % Favored : 84.16 % 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: 3.34 (0.25), residues: 1134 helix: 3.01 (0.19), residues: 762 sheet: 1.86 (0.61), residues: 76 loop : 0.09 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.011 0.001 TYR A 309 PHE 0.012 0.001 PHE B 156 TRP 0.007 0.001 TRP A 322 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8845) covalent geometry : angle 0.48473 (12038) hydrogen bonds : bond 0.06106 ( 605) hydrogen bonds : angle 3.50579 ( 1764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6498 (tpt170) cc_final: 0.5850 (pmt170) REVERT: A 301 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: A 358 GLU cc_start: 0.8753 (tt0) cc_final: 0.8312 (mt-10) REVERT: A 565 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8848 (m-30) REVERT: A 589 GLN cc_start: 0.8920 (mt0) cc_final: 0.8642 (mt0) REVERT: B 139 TRP cc_start: 0.8145 (t-100) cc_final: 0.7870 (t60) REVERT: B 286 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 388 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8216 (tp40) REVERT: B 441 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8166 (pt0) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.5698 time to fit residues: 58.1677 Evaluate side-chains 97 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3430 r_free = 0.3430 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076310 restraints weight = 13236.354| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.28 r_work: 0.2838 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.137 Angle : 0.495 9.053 12038 Z= 0.254 Chirality : 0.037 0.144 1414 Planarity : 0.004 0.053 1541 Dihedral : 7.470 83.378 1296 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.88 % Allowed : 14.06 % Favored : 84.05 % 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: 3.32 (0.25), residues: 1134 helix: 3.00 (0.19), residues: 763 sheet: 1.82 (0.60), residues: 76 loop : 0.06 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 273 TYR 0.012 0.001 TYR A 309 PHE 0.033 0.002 PHE D 59 TRP 0.006 0.001 TRP A 322 HIS 0.005 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8845) covalent geometry : angle 0.49467 (12038) hydrogen bonds : bond 0.06227 ( 605) hydrogen bonds : angle 3.51121 ( 1764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6535 (tpt170) cc_final: 0.5890 (pmt170) REVERT: A 301 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 358 GLU cc_start: 0.8758 (tt0) cc_final: 0.8316 (mt-10) REVERT: A 565 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8854 (m-30) REVERT: A 589 GLN cc_start: 0.8917 (mt0) cc_final: 0.8643 (mt0) REVERT: B 139 TRP cc_start: 0.8157 (t-100) cc_final: 0.7871 (t60) REVERT: B 286 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7898 (mm) REVERT: B 388 GLN cc_start: 0.8391 (tp-100) cc_final: 0.8188 (tp40) REVERT: B 441 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8162 (pt0) outliers start: 17 outliers final: 9 residues processed: 94 average time/residue: 0.5253 time to fit residues: 53.0230 Evaluate side-chains 96 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 50.0000 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3435 r_free = 0.3435 target = 0.104257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076544 restraints weight = 13339.079| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.29 r_work: 0.2843 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.135 Angle : 0.499 9.253 12038 Z= 0.254 Chirality : 0.037 0.143 1414 Planarity : 0.004 0.061 1541 Dihedral : 7.454 83.348 1296 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.44 % Allowed : 14.51 % Favored : 84.05 % 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: 3.34 (0.25), residues: 1134 helix: 3.02 (0.19), residues: 763 sheet: 1.81 (0.60), residues: 76 loop : 0.07 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 273 TYR 0.011 0.001 TYR A 309 PHE 0.013 0.001 PHE B 588 TRP 0.006 0.001 TRP A 322 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8845) covalent geometry : angle 0.49860 (12038) hydrogen bonds : bond 0.06163 ( 605) hydrogen bonds : angle 3.49891 ( 1764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.355 Fit side-chains REVERT: A 175 ARG cc_start: 0.6516 (tpt170) cc_final: 0.5880 (pmt170) REVERT: A 301 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: A 358 GLU cc_start: 0.8760 (tt0) cc_final: 0.8319 (mt-10) REVERT: A 565 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (m-30) REVERT: A 589 GLN cc_start: 0.8921 (mt0) cc_final: 0.8651 (mt0) REVERT: B 139 TRP cc_start: 0.8142 (t-100) cc_final: 0.7860 (t60) REVERT: B 286 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7905 (mm) REVERT: B 388 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8164 (tp40) REVERT: B 441 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: D 67 MET cc_start: 0.7572 (mmp) cc_final: 0.7335 (mtp) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.4938 time to fit residues: 47.9567 Evaluate side-chains 93 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3455 r_free = 0.3455 target = 0.105844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.078094 restraints weight = 13296.913| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.30 r_work: 0.2872 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8845 Z= 0.118 Angle : 0.478 9.300 12038 Z= 0.244 Chirality : 0.037 0.141 1414 Planarity : 0.003 0.053 1541 Dihedral : 7.245 80.291 1296 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.22 % Allowed : 14.84 % Favored : 83.94 % 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: 3.49 (0.25), residues: 1134 helix: 3.12 (0.19), residues: 762 sheet: 1.88 (0.61), residues: 76 loop : 0.16 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 273 TYR 0.021 0.001 TYR A 428 PHE 0.031 0.001 PHE D 59 TRP 0.005 0.001 TRP A 322 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8845) covalent geometry : angle 0.47833 (12038) hydrogen bonds : bond 0.05648 ( 605) hydrogen bonds : angle 3.41802 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.65 seconds wall clock time: 65 minutes 16.88 seconds (3916.88 seconds total)